What are all the calls for MatGetRow() for? They are consuming a great deal of time. Is there anyway to get rid of them?
Barry On Fri, 9 Feb 2007, Shi Jin wrote: > Sorry that is not informative. > So I decide to attach the 5 files for NP=1,2,4,8,16 > for > the 400,000 finite element case. > > Please note that the simulation runs over 100 steps. > The 1st step is first order update, named as stage 1. > The rest 99 steps are second order updates. Within > that, stage 2-9 are created for the 8 stages of a > second order update. We should concentrate on the > second order updates. So four calls to KSPSolve in the > log file are important, in stage 4,5,6,and 8 > separately. > Pleaes let me know if you need any other information > or explanation. > Thank you very much. > > Shi > --- Matthew Knepley <knepley at gmail.com> wrote: > > > You really have to give us the log summary output. > > None of the relevant > > numbers are in your summary. > > > > Thanks, > > > > Matt > > > > On 2/9/07, Shi Jin <jinzishuai at yahoo.com> wrote: > > > > > > Dear Barry, > > > > > > Thank you. > > > I actually have done the staging already. > > > I summarized the timing of the runs in google > > online > > > spreadsheets. I have two runs. > > > 1. with 400,000 finite elements: > > > > > > http://spreadsheets.google.com/pub?key=pZHoqlL60quZeDZlucTjEIA > > > 2. with 1,600,000 finite elements: > > > > > > http://spreadsheets.google.com/pub?key=pZHoqlL60quZcCVLAqmzqQQ > > > > > > If you can take a look at them and give me some > > > advice, I will be deeply grateful. > > > > > > Shi > > > --- Barry Smith <bsmith at mcs.anl.gov> wrote: > > > > > > > > > > > NO, NO, don't spend time stripping your code! > > > > Unproductive > > > > > > > > See the manul pages for > > PetscLogStageRegister(), > > > > PetscLogStagePush() and > > > > PetscLogStagePop(). All you need to do is > > maintain a > > > > seperate stage for each > > > > of your KSPSolves; in your case you'll create 3 > > > > stages. > > > > > > > > Barry > > > > > > > > On Fri, 9 Feb 2007, Shi Jin wrote: > > > > > > > > > Thank you. > > > > > But my code has 10 calls to KSPSolve of three > > > > > different linear systems at each time update. > > > > Should I > > > > > strip it down to a single KSPSolve so that it > > is > > > > > easier to analysis? I might have the code dump > > the > > > > > Matrix and vector and write another code to > > read > > > > them > > > > > into and call KSPSolve. I don't know whether > > this > > > > is > > > > > worth doing or should I just send in the > > messy > > > > log > > > > > file of the whole run. > > > > > Thanks for any advice. > > > > > > > > > > Shi > > > > > > > > > > --- Barry Smith <bsmith at mcs.anl.gov> wrote: > > > > > > > > > > > > > > > > > Shi, > > > > > > > > > > > > There is never a better test problem then > > > > your > > > > > > actual problem. > > > > > > Send the results from running on 1, 4, and 8 > > > > > > processes with the options > > > > > > -log_summary -ksp_view (use the optimized > > > > version of > > > > > > PETSc (running > > > > > > config/configure.py --with-debugging=0)) > > > > > > > > > > > > Barry > > > > > > > > > > > > > > > > > > On Fri, 9 Feb 2007, Shi Jin wrote: > > > > > > > > > > > > > Hi there, > > > > > > > > > > > > > > I am tuning our 3D FEM CFD code written > > with > > > > > > PETSc. > > > > > > > The code doesn't scale very well. For > > example, > > > > > > with 8 > > > > > > > processes on a linux cluster, the speedup > > we > > > > > > achieve > > > > > > > with a fairly large problem size(million > > of > > > > > > elements) > > > > > > > is only 3 to 4 using the Congugate > > gradient > > > > > > solver. We > > > > > > > can achieve a speed up of a 6.5 using a > > GMRes > > > > > > solver > > > > > > > but the wall clock time of a GMRes is > > longer > > > > than > > > > > > a CG > > > > > > > solver which indicates that CG is the > > faster > > > > > > solver > > > > > > > and it scales not as good as GMRes. Is > > this > > > > > > generally > > > > > > > true? > > > > > > > > > > > > > > I then went to the examples and find a 2D > > > > example > > > > > > of > > > > > > > KSPSolve (ex2.c). I let the code ran with > > a > > > > > > 1000x1000 > > > > > > > mesh and get a linear scaling of the CG > > solver > > > > and > > > > > > a > > > > > > > super linear scaling of the GMRes. These > > are > > > > both > > > > > > much > > > > > > > better than our code. However, I think the > > 2D > > > > > > nature > > > > > > > of the sample problem might help the > > scaling > > > > of > > > > > > the > > > > > > > code. So I would like to try some 3D > > example > > > > using > > > > > > the > > > > > > > KSPSolve. Unfortunately, I couldn't find > > such > > > > an > > > > > > > example either in the > > > > > > src/ksp/ksp/examples/tutorials > > > > > > > directory or by google search. There are a > > > > couple > > > > > > of > > > > > > > 3D examples in the > > > > src/ksp/ksp/examples/tutorials > > > > > > but > > > > > > > they are about the SNES not KSPSolve. If > > > > anyone > > > > > > can > > > > > > > provide me with such an example, I would > > > > really > > > > > > > appreciate it. > > > > > > > Thanks a lot. > > > > > > > > > > > > > > Shi > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > > > > > Finding fabulous fares is fun. > > > > > > > Let Yahoo! FareChase search your favorite > > > > travel > > > > > > sites to find flight and hotel bargains. > > > > > > > > > > > > > http://farechase.yahoo.com/promo-generic-14795097 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > ____________________________________________________________________________________ > > > > > 8:00? 8:25? 8:40? Find a flick in no time > > > > > with the Yahoo! Search movie showtime > > shortcut. > > > > > http://tools.search.yahoo.com/shortcuts/#news > > > > > > > > === message truncated === > > > > > ____________________________________________________________________________________ > Finding fabulous fares is fun. > Let Yahoo! FareChase search your favorite travel sites to find flight and > hotel bargains. > http://farechase.yahoo.com/promo-generic-14795097
